Variant report

Variant	rs304723
Chromosome Location	chr19:44102338-44102339
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:44102199-44102351	HepG2	liver:	n/a	n/a
2	POLR2A	chr19:44099844-44102464	SK-N-MC	brain:	n/a	n/a
3	POLR2A	chr19:44102309-44102385	HUVEC	blood vessel:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:44077678..44083171-chr19:44093489..44103015,14	K562	blood:
2	chr19:44077687..44082496-chr19:44098234..44103069,7	MCF-7	breast:
3	chr19:44098671..44105555-chr19:44121892..44125342,15	MCF-7	breast:
4	chr19:44098885..44105672-chr19:44139703..44145307,6	MCF-7	breast:
5	chr19:44097777..44104240-chr19:44121602..44130880,30	K562	blood:
6	chr19:44101670..44103492-chr19:44107059..44108577,2	MCF-7	breast:
7	chr19:44100992..44104093-chr19:44119148..44120939,3	K562	blood:
8	chr19:44100944..44102513-chr19:44136939..44138687,2	MCF-7	breast:
9	chr19:44097500..44104541-chr19:44116930..44130620,31	K562	blood:
10	chr19:44101681..44103493-chr19:44106654..44108776,2	K562	blood:
11	chr19:44036790..44040633-chr19:44098075..44102401,5	K562	blood:
12	chr19:44036790..44039764-chr19:44099068..44102401,4	K562	blood:

No data

Variant related genes	Relation type
IRGQ	TF binding region
ENSG00000073050	Chromatin interaction
ENSG00000105767	Chromatin interaction
ENSG00000176472	Chromatin interaction
ENSG00000234465	Chromatin interaction
ENSG00000131116	Chromatin interaction
ENSG00000269583	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10402946	0.92[ASW][hapmap];0.97[LWK][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes]
rs17655646	0.86[CEU][hapmap]
rs2240633	1.00[CEU][hapmap];0.98[GIH][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2270075	0.89[AFR][1000 genomes]
rs304719	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs304720	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs304722	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs304726	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34521657	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34637472	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35346236	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs365063	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3803910	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs427115	0.93[ASW][hapmap];1.00[CEU][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4803646	0.82[CEU][hapmap]
rs4803647	0.83[EUR][1000 genomes]
rs7245651	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8101956	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532821	chr19:43842383-44357315	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv833839	chr19:44099813-44272299	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs304723	STRN4	cis	cerebellum	SCAN
rs304723	PRRG2	cis	cerebellum	SCAN
rs304723	IZUMO2	cis	parietal	SCAN
rs304723	ELSPBP1	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44098800-44102400	Active TSS	HUES64 Cell Line	embryonic stem cell
2	chr19:44100600-44102400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
3	chr19:44100600-44102400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr19:44100600-44102400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr19:44100800-44102400	Flanking Active TSS	Duodenum Mucosa	Duodenum
6	chr19:44100800-44102400	Flanking Active TSS	HUVEC	blood vessel
7	chr19:44100800-44102600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
8	chr19:44101000-44102400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr19:44101000-44102400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr19:44101000-44102400	Flanking Active TSS	K562	blood
11	chr19:44101000-44102400	Flanking Active TSS	Osteobl	bone
12	chr19:44101200-44102400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr19:44101200-44102400	Flanking Active TSS	NHLF	lung
14	chr19:44101200-44102600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr19:44101400-44102400	Enhancers	Fetal Brain Male	brain
16	chr19:44101400-44102400	Enhancers	Sigmoid Colon	Sigmoid Colon
17	chr19:44101400-44102400	Flanking Active TSS	A549	lung
18	chr19:44101400-44102600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr19:44101400-44103000	Weak transcription	Ovary	ovary
20	chr19:44101600-44102400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr19:44101600-44102400	Enhancers	Primary B cells from peripheral blood	blood
22	chr19:44101600-44102400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
23	chr19:44101600-44102400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr19:44101600-44102400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr19:44101600-44102400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
26	chr19:44101600-44102400	Enhancers	Colonic Mucosa	Colon
27	chr19:44101600-44102400	Enhancers	Pancreas	Pancrea
28	chr19:44101600-44102600	Weak transcription	Left Ventricle	heart
29	chr19:44101600-44102600	Enhancers	Stomach Mucosa	stomach
30	chr19:44101600-44102800	Enhancers	Primary T cells fromperipheralblood	blood
31	chr19:44101600-44102800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
32	chr19:44101600-44102800	Weak transcription	Aorta	Aorta
33	chr19:44101600-44103600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr19:44101600-44112000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr19:44101800-44102400	Enhancers	iPS-15b Cell Line	embryonic stem cell
36	chr19:44101800-44102400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr19:44101800-44102400	Enhancers	Cortex derived primary cultured neurospheres	brain
38	chr19:44101800-44102400	Enhancers	Fetal Heart	heart
39	chr19:44101800-44102400	Enhancers	Fetal Lung	lung
40	chr19:44101800-44102400	Enhancers	Fetal Thymus	thymus
41	chr19:44101800-44102400	Enhancers	Rectal Smooth Muscle	rectum
42	chr19:44101800-44102400	Enhancers	Thymus	Thymus
43	chr19:44101800-44102600	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr19:44101800-44102600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr19:44101800-44102600	Enhancers	Breast Myoepithelial Primary Cells	Breast
46	chr19:44101800-44102600	Enhancers	Primary B cells from cord blood	blood
47	chr19:44101800-44102600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
48	chr19:44101800-44102600	Enhancers	Primary T helper naive cells from peripheral blood	blood
49	chr19:44101800-44102600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
50	chr19:44101800-44102600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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